AnGenMap

Archived Post

From listmasteranimalgenome.org  Mon Jan  3 17:29:00 2022
Return-Path: <listmasteranimalgenome.org>
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
Postmaster: submission approved by list moderator
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: What's new on the NAGRP animal genome web site (#1, 2022)
Date: Mon, 03 Jan 2022 17:29:00 -0600

What's new on the NAGRP animal genome web site (#1, 2022)

o Animal QTLdb and CorrDB updates -- Announcing a joint release of the
  QTLdb (Release 46) and CorrDB (Release 14):

  (Dec 27, 2021): A sum of 15,569 new QTL/associations have been curated
  into the database. (New additions less obsolete/retracted ones:
  Catfish: 0; Cattle: 13,474; Chicken: 796; Goat: 4; Horse: 132; Pig: 802;
  Sheep: 320; Rainbow trout: 41 -- Net increase: 15,569). The current total
  number of QTL in the database: 235,970 [Breakdown: Cattle: 177,199;
  Chicken: 16,271; Goat: 68; Horse: 2,605; Pig: 34,342; Sheep: 4,072;
  Rainbow trout: 1,413], curated from 2,554 publications.

  URL: https://www.animalgenome.org/QTLdb

  (Dec 27, 2021): A sum of 552 new correlations [Breakdown by species --
  Pig: 420 (6 new traits); Cattle: 30 (1 new trait); Sheep: 102 (1 new
  trait)] and a sum of 46 new heritability data [Breakdown by species --
  Pig: 3 (0 new traits); Cattle: 23 (5 new traits); Chicken: 1 (0 new
  traits); Horse: 4 (0 new traits); Sheep: 15 (1 new trait)] have been
  curated into the CorrDB.  To date, the total number of correlation data
  in the database: 24,104 [Breakdown by species -- Cattle: 12,831; Chicken:
  1,455; Horse: 209; Pig: 7,581; Sheep: 1,717], and total heritability
  data: 4,319 [Breakdown by species -- Cattle: 2,196; Chicken: 319; Horse:
  122; Pig: 1,447; Sheep: 233], curated from 344 publications.

  URL: https://www.animalgenome.org/CorrDB

  Database developments:

  (1) New database developments have been highlighted in our recent paper
  published in the 2022 Database Issue of Nucleic Acids Research, "Bringing
  the Animal QTLdb and CorrDB into the future: meeting new challenges and
  providing updated services", that include (a) A standardized protocol for
  adding new species to QTLdb/CorrDB; (b) A livestock SNP ID/name matching
  repository to assist SNP-based data curation; (c) A pipeline for mapping
  QTL/association data to a genome build, enabling QTLdb support for
  multiple assemblies within a species; and (d) Extensive web portal
  revisions and web interface redevelopment in order to accommodate new
  tools while facilitating a straightforward user experience on the web
  portal.

  (2) New funding from USDA/NIFA for the next 3 years will facilitate our
  efforts to not only maintain the current level of database updates of
  the Animal QTLdb and CorrDB, but also to explore new frontiers in terms
  of accelerated data curation using automated text mining for data
  incorporation, and to improve the ontology tools for data dissemination.


o FAANG website updates

  A "new updates and activities" ball icon was added to the FAANG website
  that automatically generates bullet points for new items/areas on the
  website within 30 days. The most active sections on the website are (1)
  membership updates; (2) working committee membership updates; (3) steering
  committee communications; and (4) list of new publications by the community
  members.

  URL: https://www.faang.org/


o Ontology developments:

  (1) Five updates were made to the Vertebrate Trait (VT) Ontology data
      (versions 11.11, 11.12, 11.13, 11.14, and 11.15).
  (2) Two updates were made to the Livestock Product Trait (LPT) ontology
      (versions 3.1 and 3.2).


o Data repository:

  We have entered the last phase of the transition from hosting supplementary
  data for publications at AnimalGenome.ORG to using the Open Science
  Framework (OSF, https://osf.io/) for best use of our resources.  We will
  start to transfer the current data to OSF in the coming months and forward
  the data visits to their new home as long as AnimalGenome.ORG is in service.

  In the meantime, we encourage users to directly use the OSF.
  URL: https://www.animalgenome.org/repository/pub/


Check out the daily "what's new" (https://www.animalgenome.org/news/) items
for more up-to-date information on this site. Thanks in advance for kindly
reporting broken links/errors, or suggesting corrections on our site.

Your input is always appreciated. Feel free to contact us at any time with
your needs, requests, and/or suggestions: Jim Reecy (jreecyiastate.edu),
James Koltes (jekoltesiastate.edu), Fiona McCarthy (fionamccarizona.edu).
Or talk to us using our Helpdesk (https://www.animalgenome.org/helpdesk).

--
NAGRP Bioinfo Team
bioinfo-teamanimalgenome.org


 
© 2003-2022 USA · USDA · NAGRP · Bioinformatics Coordination Program.
Contact: NAGRP Bioinformatics Team
Helpdesk